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Protein

Pyridoxal 5'-phosphate synthase subunit PdxT

Gene

pdxT

Organism
Geobacillus kaustophilus (strain HTA426)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS.UniRule annotation

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.UniRule annotation
L-glutamine + H2O = L-glutamate + NH3.UniRule annotation

Pathwayi: pyridoxal 5'-phosphate biosynthesis

This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei78 – 781NucleophileUniRule annotation
Binding sitei105 – 1051L-glutamineUniRule annotation
Active sitei169 – 1691Charge relay systemUniRule annotation
Active sitei171 – 1711Charge relay systemUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Lyase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciGKAU235909:GJO7-17-MONOMER.
UniPathwayiUPA00245.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal 5'-phosphate synthase subunit PdxTUniRule annotation (EC:4.3.3.6UniRule annotation)
Alternative name(s):
Pdx2UniRule annotation
Pyridoxal 5'-phosphate synthase glutaminase subunitUniRule annotation (EC:3.5.1.2UniRule annotation)
Gene namesi
Name:pdxTUniRule annotation
Ordered Locus Names:GK0012
OrganismiGeobacillus kaustophilus (strain HTA426)
Taxonomic identifieri235909 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
Proteomesi
  • UP000001172 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 196196Pyridoxal 5'-phosphate synthase subunit PdxTPRO_0000135639Add
BLAST

Interactioni

Subunit structurei

In the presence of PdxS, forms a dodecamer of heterodimers. Only shows activity in the heterodimer.UniRule annotation

Protein-protein interaction databases

STRINGi235909.GK0012.

Structurei

Secondary structure

1
196
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Beta strandi8 – 114Combined sources
Helixi12 – 2110Combined sources
Beta strandi25 – 317Combined sources
Helixi32 – 354Combined sources
Beta strandi39 – 435Combined sources
Helixi48 – 5710Combined sources
Helixi61 – 699Combined sources
Beta strandi74 – 774Combined sources
Helixi79 – 846Combined sources
Beta strandi85 – 884Combined sources
Beta strandi99 – 1046Combined sources
Turni105 – 1084Combined sources
Helixi111 – 1133Combined sources
Beta strandi115 – 1195Combined sources
Beta strandi128 – 1347Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi146 – 1516Combined sources
Beta strandi154 – 1607Combined sources
Beta strandi163 – 1686Combined sources
Helixi170 – 1723Combined sources
Helixi177 – 18812Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4WXYX-ray2.70B/D/F/H/J/L1-196[»]
ProteinModelPortaliQ5L3Y1.
SMRiQ5L3Y1. Positions 1-196.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni46 – 483L-glutamine bindingUniRule annotation
Regioni133 – 1342L-glutamine bindingUniRule annotation

Sequence similaritiesi

Belongs to the glutaminase PdxT/SNO family.UniRule annotation

Keywords - Domaini

Glutamine amidotransferase

Phylogenomic databases

eggNOGiENOG4108UHX. Bacteria.
COG0311. LUCA.
HOGENOMiHOG000039949.
KOiK08681.
OMAiVYGTCAG.
OrthoDBiEOG66F0BW.

Family and domain databases

Gene3Di3.40.50.880. 1 hit.
HAMAPiMF_01615. PdxT.
InterProiIPR029062. Class_I_gatase-like.
IPR002161. PdxT/SNO.
IPR021196. PdxT/SNO_CS.
[Graphical view]
PfamiPF01174. SNO. 1 hit.
[Graphical view]
PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
SUPFAMiSSF52317. SSF52317. 1 hit.
TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
PROSITEiPS01236. PDXT_SNO_1. 1 hit.
PS51130. PDXT_SNO_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5L3Y1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIGVLGLQG AVREHVRAIE ACGAEAVIVK KPEQLEGLDG LVLPGGESTT
60 70 80 90 100
MRRLIDRYGL MEPLKQFAAA GKPMFGTCAG LILLAKRIVG YDEPHLGLMD
110 120 130 140 150
ITVERNSFGR QRESFEAELS IKGVGDGFVG VFIRAPHIVE AGDGVDVLAT
160 170 180 190
YNDRIVAARQ GQFLGCSFHP ELTDDHRLMQ YFLNMVKEAK MASSLK
Length:196
Mass (Da):21,374
Last modified:February 1, 2005 - v1
Checksum:iD94022298F7F5AB5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD74297.1.
RefSeqiWP_011229528.1. NC_006510.1.

Genome annotation databases

EnsemblBacteriaiBAD74297; BAD74297; GK0012.
GeneIDi3185183.
KEGGigka:GK0012.
PATRICi21961029. VBIGeoKau81518_0057.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000043 Genomic DNA. Translation: BAD74297.1.
RefSeqiWP_011229528.1. NC_006510.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4WXYX-ray2.70B/D/F/H/J/L1-196[»]
ProteinModelPortaliQ5L3Y1.
SMRiQ5L3Y1. Positions 1-196.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi235909.GK0012.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD74297; BAD74297; GK0012.
GeneIDi3185183.
KEGGigka:GK0012.
PATRICi21961029. VBIGeoKau81518_0057.

Phylogenomic databases

eggNOGiENOG4108UHX. Bacteria.
COG0311. LUCA.
HOGENOMiHOG000039949.
KOiK08681.
OMAiVYGTCAG.
OrthoDBiEOG66F0BW.

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciGKAU235909:GJO7-17-MONOMER.

Family and domain databases

Gene3Di3.40.50.880. 1 hit.
HAMAPiMF_01615. PdxT.
InterProiIPR029062. Class_I_gatase-like.
IPR002161. PdxT/SNO.
IPR021196. PdxT/SNO_CS.
[Graphical view]
PfamiPF01174. SNO. 1 hit.
[Graphical view]
PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
SUPFAMiSSF52317. SSF52317. 1 hit.
TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
PROSITEiPS01236. PDXT_SNO_1. 1 hit.
PS51130. PDXT_SNO_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus."
    Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H., Matsui S., Uchiyama I.
    Nucleic Acids Res. 32:6292-6303(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HTA426.

Entry informationi

Entry nameiPDXT_GEOKA
AccessioniPrimary (citable) accession number: Q5L3Y1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: February 1, 2005
Last modified: November 11, 2015
This is version 64 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.